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AmphoraVizu, Chart visualization for metagenomics analysis tools AMPHORA2 and AmphoraNet by Csaba Kerepesi, Balázs Szalkai, Vince Grolmusz PIT Bioinformatics Group, http://pitgroup.org/ ***Terms of Use:*** AmphoraVizu is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details: <http://www.gnu.org/licenses/>. ***Help:*** - User Manual for AmphoraVizu: http://www.pitgroup.org/static/AmphoraVizu-Manual.pdf - For any other inquiries send an Email to Csaba Kerepesi: kerepesics@gmail.com - AmphoraVizu webserver: http://pitgroup.org/amphoravizu ***Quick start:*** 1. Open Source AmphoraVizu is a program written in Perl programming language. Perl is downloadable from https://www.perl.org/get.html 2. Use an AMPHORA2 or AmphoraNet output file as input file (sample files are available here: http://www.pitgroup.org/static/amphora2_results/ ) 3. A typical command: perl AmphoraVizu.pl -input example_output.txt -min_confidence 0.1 -lowest_rank 2 -min_average 0.02 -chart_type column > out.html 4. Finally open the out.html file in a web browser. ***Options:*** -input: input file (AMPHORA2 output file), default: /dev/stdin -min_confidence: minimum confidence, default: 0.1 -lowest_rank: lowest rank (1=Superkingdom, 7=Species), default: 2 -min_average: minimum average to display, default: 0.02 -chart_title: chart title (with optional HTML tags), to override default title -chart_type: "column": Column Chart output (default), "pie": Pie chart output with averages -chart_width: width of chart area, all CSS values are valid (default: 100%) -chart_height: height of chart area (default: 100%) -chart_compact: if 1, margins are decreased as much as possible (default: 0) -html_inline: if 1, tags like <html>, <head> and <body> are omitted (default: 0) -miniview: 1: miniview on, 0: miniview off (default: 0) -sort: "avg": sorted by averages (default), "abc" sorted by alphabet -quantify: "prop": shows the proportions of marker genes (default), "amounts": shows the exact amounts of marker genes